Fluffwise, for the airforce you are talking an imperial naval squadron assigned to a specific guard regiment as their air support. They adopt to color patterns of either a.) The theatre appropriate camouflage or b.) Adopt the pattern of the unit they are assigned to.
There is a good explanation in the codex I believe
Those are two good ways to have a united color scheme. I'm assuming the aircraft will be detached to your unit for a long stay? If so, they will be reporting to your regimental commander, and the extra armor would be added that makes them skimmers rather than true flyers. For such a long term assignment, a paint job would be in character.
Also, dark blue and black might possibly be a navy uniform pattern. While the Navy is not supposed to have enough ground force to support an insurrection, one occasionally sees players running an Imperial Guard or Demon Hunter force as a naval detachment.
But do what makes you happy. One can find fluff to justify many approaches. Generally, I'd recommend a unified paint scheme, but my own Guard force can at best be described as 'irregulars.' Most of my force started as chaos cultists, as civilians given weapons at last moment, fighting out of desperation. Thus, I'm in no position to say one approach is the true approach. Whatever fits.